Altering a trait in a plant has long been a desired goal. For example, elongated fruit is an important property in tomato from cultural and agronomical points of view. Tomatoes that are mechanically harvested and used for canning as well as the preparation of sauces typically feature elongated and blocky fruits. These shape characters are important to prevent the tomatoes to roll of conveyer belts during machine harvesting. Whole rectangular shaped tomatoes fit better in a can than when they are round in shape. Furthermore, the recent development of new varieties for fresh consumption resulted in an expansion of novel fruit shapes in this class of tomatoes. Perhaps most notable of these are the grape tomatoes which feature the size of a cherry tomato but the fruits are oval instead of round shaped. In addition to other improved qualities such as flavor and aroma, the distinct shape of the fruit makes it easy for consumers to separate the cherry and the grape tomatoes. The elongated fruit shape features undoubtedly led to the rapid increase in popularity of grape tomato in the last five years.
The molecular bases underlying fruit shape variation in plant species are largely unknown. Fruit crops display tremendous diversity in the morphology of the reproductive organ in comparison to their wild relatives. Wild relatives of tomato bear small and round fruit, while cultivated types bear fruit of increased size and many diverse shapes including flattened, rectangular and blocky, oxheart, bell pepper, long pepper and pear forms. This morphological variation is controlled by genetic loci that have major as well as minor effects1-5.
A prevalent morphological feature that distinguishes many cultivated tomatoes from undomesticated accessions is elongated fruit shape. Three major loci affect this feature: ovate, fs8.1, and sun, residing on chromosomes 2, 8, and 7, respectively. OVATE, which confers an elongated pear shape to fruit encodes a protein that negatively regulates plant growth6. The locus fs8.1 imparts an elongated blocky shape to fruit, while sun imparts an elongated and tapered shape to fruit1, 4, 8.
The locus sun comprises a major QTL and explains 58% of the phenotypic variation associated with elongated fruit shape in an F2 population derived from elongated-fruited S. lycopersicum variety ‘Sun1642’ and the small round-fruited wild relative S. pimpinellifolium, accession LA15898. Fine mapping indicates that sun resides in a dynamic region of the tomato genome where a large inversion comprising half of the short arm of chromosome 7, and small-scale insertions, deletions and tandem duplications distinguish the species in the tomato clade9. One insertion, estimated to be 30 kb, is particularly noteworthy because it is present in Sun1642 but not in LA1589, and is linked to fruit shape9.
Structural variations of genomes, such as duplications, deletions, inversions, and translocations, are prevalent in man and some of these variants underlie diseases10-12. The structural variants are named copy number variants if they comprise a region larger than 500 bp-1 kb but smaller than 3-5 Mb10, 11. Although the molecular mechanisms facilitating genome rearrangements resulting in copy number variants are often unknown, non-allelic homologous recombination is most commonly proposed.
In plants, the occurrence and extent of copy number variants and the role this type of structural variation plays in affecting phenotypic diversity within a species are largely unknown. The lack of information about structural variation within plant species is due to the lack of complete whole genome sequence information of accessions within the same species.
In addition to non-allelic homologous recombination, transposing elements can also create structural variations of genomes13, 14. Most notably, the transposition can lead to dramatic changes in phenotype when these elements land in the gene thereby inactivating its function. In fact, the ability of transposable elements to knock out host gene activity has been used extensively in functional analyses studies in many species.
An unusual group of transposable elements was discovered recently which were found to harbor segments of the host's genome. Of particular note are the Helitron and Pack-MULE DNA transposable elements found in maize, rice, and many other species15-20. These elements are unusual in that they ferry host gene and gene fragments around and have the potential to create novel proteins and protein functions through domain shuffling. Also, certain types of retroelements have the potential to create novel genes by read-through transcription into host genes followed by transposition of the element and its transduced segment elsewhere in the genome. Although this type of transposition is not often described in plants, the L1 retroelement is thought to be responsible for transducing up to 1% of the human genome21. Another transposon-like mechanism with the ability to generate novel functions is through the fortuitous reverse transcription of host mRNAs and the subsequent random insertion of these cDNA molecules into the genome. Although it is generally thought that most of these so-called retrogenes are non-functional, they have the potential to generate considerable phenotypic diversity in both plant and animals22 and provide one of the mechanisms for gene family expansion over evolutionary time23.
However, despite the potential of these latter types of transposable elements to underlie phenotypic variation via either the creation of novel genes, altering their expression through repositioning them in different chromosomal contexts, or by generating small interfering RNA that participate in silencing of host genes13, 14, 24, documented examples of a change in phenotype as a direct result of these types of transposition do not exist.